Proportional editing problem
Add a cube, and position it so that its lower face sits where you'd like the cylinder's vertices to be. The tip of the cylinder should be inside the cube.



Select the cylinder. In the Modifier Properties tab, on the right-hand side pannel, add a Boolean modifier. Make sure it's set to Difference and, under object, select the cube (be aware that there might be many cubes in your scene; make sure to select the right one).



Your cylinder should now bear a cut as the one you described. If evertyhing seems to be in order, hit Apply in the boolean modifier and get rid of the cube.